Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We have devised a molecular model building computer program (DEZYMER) which builds new ligand binding sites into a protein of known three-dimensional structure. It alters only the sequence and the side-chain structure of the protein, leaving the protein backbone fold intact by definition. The program searches for a constellation of backbone positions arranged such that if appropriate side-chains were placed there, they would bind the ligand according to a pre-defined geometry of interaction specified by the experimentalist. These binding sites are introduced by the program by taking into account simple rules such as steric hindrance, atomic close-packing and hydrogen bond patterns, which are known to maintain the integrity of a protein structure to a first approximation. A test case is presented in this paper where the copper binding site found in blue-copper proteins such as plastocyanin, azurin and cupredoxin is introduced into Escherichia coli thioredoxin. The model building of one of the solutions found by the program is presented in some detail. The experimental construction and properties of this new protein are described in an accompanying paper. It is hoped that this program provides a general method for the design of ligand binding sites and enzyme active sites, which can then be tested experimentally.
J Mol Biol 1991 Dec 05
PMID:Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. 174

Podophyllotoxin (PD) and its derivative etoposide (VP-16), a clinically useful anticancer drug, exhibit different mechanisms of action. PD binds specifically to tubulin to prevent its polymerization, whereas VP-16 lacks this action. The DNA strand breakage caused by VP-16 is thought to be due to its interaction with topoisomerase II or to free radical formation by oxidation of its 4'-phenolic hydroxyl group to a semiquinone free radical. We have demonstrated that PD, VP-16, 4'-demethylepipodophyllotoxin (DEPD), and syringic acid (SA) exhibit no DNA-cleaving activity but, in the presence of metal ions such as Cu2+ and Fe3+, DEPD and SA form metal complexes, which in turn show high activity for DNA strand scission at pH 7.8 under air. Furthermore, it was found that DNA cleavage was greatly promoted by irradiation with UV light. The PD-Fe3+ system at pH 7.8 showed very low DNA-cleaving activity, but irradiation with UV light in the system induced almost complete DNA breakage. DNA cleavages were significantly inhibited in the presence of hydroxyl radical scavengers, such as sodium benzoate and dimethylurea, in the Cu(2+)-SA and Fe(3+)-PD systems, with or without UV irradiation. These reactions were investigated by optical and ESR spectra, coupled with ESR spin-trapping techniques, by which the formation of hydroxy radicals was clearly detected in all systems. These findings have led us to a new proposal of the metal- and photo-induced mechanism for understanding the antitumor action of PD, VP-16, and their related compounds.
Mol Pharmacol 1991 Dec
PMID:Metal- and photo-induced cleavage of DNA by podophyllotoxin, etoposide, and their related compounds. 175 45

A three-dimensional model of the "blue" copper-glycoprotein stellacyanin from Rhus vernicifera has been derived by computer graphics, energy minimization and molecular dynamics techniques. The initial atomic co-ordinates were obtained by making substitutions and insertions in the known structure of another blue copper-protein, cucumber basic protein (CBP), which is 46% homologous with stellacyanin and has similar spectroscopic properties. An important difference between CBP and stellacyanin is that the latter lacks methionine, a residue that forms an exceptionally long bond to the copper atom in all blue copper-proteins of known structure. In the aligned amino acid sequences, stellacyanin has glutamine 97 at the position that corresponds to the copper-binding methionine 89 in CBP. The hypothesis that the copper atom in stellacyanin is co-ordinated by the side-chain functional groups of histidine 46, cysteine 87, histidine 92 and glutamine 97 leads to a model that enables the spectroscopic properties, redox potential and electron-transfer kinetics of the protein to be rationalized. The present model for stellacyanin is more plausible than an antecedent model derived from the structure of plastocyanin. This demonstrates that the output from molecular modeling calculations is strongly dependent on the input, and that sequence homology with the target molecule is an important criterion for the selection of a starting model.
J Mol Biol 1991 Dec 20
PMID:Three-dimensional model for stellacyanin, a "blue" copper-protein. 176 45

A relatively recent method developed to determine the molecular weights of intact peptides and proteins, matrix-assisted UV laser desorption time-of-flight mass spectrometry (LDTOF-MS), has been evaluated as a new means to investigate the metal ion-binding properties of model synthetic peptides. A contiguous sequence of 25 residues on the surface of the 74 kDa human plasma metal-binding transport protein histidine-rich glycoprotein (HRG) has been identified as a bioactive metal-binding domain. The peptide, (GHHPH)5G, was synthesized and evaluated by LDTOF-MS before and after the addition of Cu(II) in solution with 2,5-dihydroxybenzoic acid as the matrix. In the absence of added Cu(II), the major protonated molecular ion (M + H)+ was observed to have a mass equal to its calculated mass (2904.0 Da). In the presence of Cu(II), however, five additional peaks were observed at mass increments of approximately 63.9 Da. The maximum Cu(II)-binding capacity observed for the 26-residue peptide (5 g-atoms/mol) suggested that up to 1 Cu(II) may be bound per 5-residue internal repeat unit (GHHPH) within this peptide; several other monovalent and divalent metal cations were not bound under identical conditions of analysis. The Cu(II)-binding stoichiometry was verified by spectrophotometric titration and by frontal analyses of the immobilized peptide with a solution of Cu(II) ions. These results demonstrate the ability to verify directly the solution-phase binding capacity of metal-binding peptides by LDTOF-MS.
J Mol Recognit
PMID:Evaluation of peptide/metal ion interactions by UV laser desorption time-of-flight mass spectrometry. 179 64

Coronary thrombolysis is the treatment of choice for patients with acute Q wave myocardial infarcts who have no contraindication to such therapy. However, the time required for thrombolysis to occur and the possibility of reocclusion of the infarct-related artery following thrombolytic therapy are problems. The time required for thrombolysis to occur with currently available agents ranges from 40 to 60 minutes and the frequency of reocclusion of the infarct-related artery after tissue-type plasminogen activator is 10 to 20%. We review experimental studies and clinical evaluations in which attempts have been made to develop adjunctive therapies that when coupled with available thrombolytic interventions might shorten the time to thrombolysis and delay or prevent reocclusion. From the studies done to date, it appears that a combination of thromboxane synthesis inhibitor and receptor antagonist with a serotonin receptor antagonist and heparin shortens the time to thrombolysis and delays or prevents coronary artery reocclusion in experimental canine models with copper coil-induced coronary artery thrombi. A monoclonal antibody to the platelet glycoprotein IIb/IIIa receptor given with tissue plasminogen activator and heparin also shortens the time to thrombolysis and delays or prevents reocclusion in experimental canine models. A mutant tissue plasminogen activator with a glycosylation defect and prolonged systemic clearance delays coronary artery reocclusion following lysis of three-hours coronary thrombi, induced by a copper coil. Thrombin inhibitors, including heparin, and synthetic inhibitors, given with tissue plasminogen activator and aspirin, appear to shorten the time to thrombolysis and delay or prevent coronary artery reocclusion in experimental canine models.(ABSTRACT TRUNCATED AT 250 WORDS)
Mol Biol Med 1991 Apr
PMID:Thrombolytic therapy: enhancement by platelet and platelet-derived mediator antagonists. 180 65

The purified Ca2+/Mg2+ ATPase from rat heart plasma membrane was activated by Ca2+ and Mg2+ with Ka values of 1.47 mM and 2.51 mM, respectively; other divalent cations also activated the enzyme but to a lesser extent. Divalent cations like Cu2+, Zn2+, Ni2+, Cd2+ were potent inhibitors of the enzyme activity in the presence of Ca2+ or Mg2+ whereas Na+, K+ or HCO3- did not affect the Ca2+/Mg2+ ATPase activity; the pH optima was 8.5. The enzyme hydrolyzed ATP with a Km of 0.34 mM for Ca2+ ATPase and 0.48 mM for Mg2+ ATPase; various nucleoside triphosphate such as ITP, CTP, GTP, and UTP were also hydrolyzed. Phospholipase A and C as well as neuraminidase decreased the Ca2+/Mg2+ ATPase activity whereas phospholipase D was ineffective. The purified Ca2+/Mg2+ ATPase was found to bind ATP-r-35S with two affinities; the KD values were 50.9 +/- 0.8 and 1160 +/- 198 nM and the Bmax values were 8.71 +/- 0.16 and 145 +/- 9.7 nmol/mg protein for high and low affinity sites, respectively. Treatment of the enzyme preparation with phospholipases and neuraminidase did not affect the ATP-r-35S binding. Ca2+ was also found to bind with Ca2+/Mg2+ ATPase with a KD of 0.384 mM and a Bmax of 1.85 mumol/mg protein; Ni2+, Mn2+, Zn2+ at 1 mM concentrations inhibited the Ca2+ binding but Mg2+ and verapamil were without effect. Phospholipase A and neuraminidase decreased the Ca2+ binding by 20-30%; this indicated that Ca2+ binding with the purified enzyme may be partly due to the phospholipids and sialic acid residues associated with the enzyme. These results show that the purified Ca2+/Mg2+ ATPase is a Ca2+ binding glycoprotein having two binding sites for ATP. Furthermore, this study suggests that phospholipids associated with purified Ca2+/Mg2+ ATPase are required for maximal activity.
Mol Cell Biochem 1991 Oct 16
PMID:Characterization of the purified rat heart plasma membrane Ca2+/Mg2+ ATPase. 183 90

Cytochrome c-oxidase type aa3 (EC 1.9.3.1) was purified to homogeneity from vegetative Bacillus cereus by ion-exchange and hydroxylapatite chromatography in the presence of Triton X-100. Gel filtration analysis suggested a dimeric structure apparently 172 kDa in size; however, only a monomer of 81 kDa was detected when analysed by non-denaturing gel electrophoresis. Denaturing gel electrophoresis analysis of the protein showed the presence of two subunits (51 and 30 kDa). Atomic absorption and visible spectroscopy showed typical aa3 redox centres with haem a iron and copper in a ratio of 22 nmol and 35 ng-atom per mg protein, respectively. No haem c was found associated with the purified enzyme in the conditions reported here. Oxidase activity was fully reconstituted by phospholipids in the presence of N,N,N',N'-tetramethyl-p-phenylenediamine or reduced yeast cytochrome c (but not horse cytochrome c) as electron donors. This activity was abolished by cyanide and carbon monoxide.
Mol Microbiol 1991 Jan
PMID:Purification and characterization of two-subunit cytochrome aa3 from Bacillus cereus. 184 7

Redox inactivation of glutathione reductase involves metal cations, since chelators protected against NADPH-inactivation, 3 microM EDTA or 10 microM DETAPAC yielding full protection. Ag+, Zn2+ and Cd2+ potentiated the redox inactivation promoted by NADPH alone, while Cr3+, Fe2+, Fe3+, Cu+, and Cu2+ protected the enzyme. The Zn2+ and Cd2+ effect was time-dependent, unlike conventional inhibition. Glutathione reductase interconversion did not require dioxygen, excluding participation of active oxygen species produced by NADPH and metal cations. One Zn2+ ion was required per enzyme subunit to yield full NADPH-inactivation, the enzyme being reactivated by EDTA. Redox inactivation of glutathione reductase could arise from the blocking of the dithiol formed at the active site of the reduced enzyme by metal cations, like Zn2+ or Cd2+. The glutathione reductase activity of yeast cell-free extracts was rapidly inactivated by low NADPH or moderate NADH concentrations; NADP+ also promoted rapid inactivation in fresh extracts, probably after reduction to NADPH. Full inactivation was obtained in cell-free extracts incubated with glucose-6-phosphate or 6-phosphogluconate; the inactivating efficiency of several oxidizable substrates was directly proportional to the specific activities of the corresponding dehydrogenases, confirming that redox inactivation derives from NADPH formed in vitro.
Mol Cell Biochem 1991 Mar 13
PMID:Metals are directly involved in the redox interconversion of Saccharomyces cerevisiae glutathione reductase. 186 75

The interaction of acidic copper-containing protein from the membranes of chromaffin granules has been investigated with cytochrome b-561 and dopamine-beta-monooxygenase from the same source. By the use of spectral and polarographic measurements it was demonstrated that the acidic copper-containing protein acts as an electron acceptor for cytochrome b-561 and as electron donor in the reactions, catalyzed by dopamine-beta-monooxygenase. According to the data obtained the possible function of the acidic copper-containing protein in vivo on the area of electron transfer chain between cytochrome b-561 and dopamine-beta-monooxygenase are discussed. The activation or inhibition of the electron transfer reactions by a variety of phospholipids, analogs of membrane lipids of chromaffin granules has been established. The experiments were performed in a model systems by the use of highly purified preparations of proteins and bilamellar liposomes and micelles, prepared from the corresponding phospholipids.
Mol Biol (Mosk)
PMID:[Acidic copper-containing proteins--an intermediate link to the electron transfer stage from cytochrome b-561 to dopamine-beta-monooxygenase]. 189 44

Superoxide dismutases (SOD) play a major role in the intracellular defense against oxygen radical damage to aerobic cells. In eucaryotes, the cytoplasmic form of the enzyme is a 32-kDa dimer containing two copper and two zinc atoms (CuZn SOD) that catalyzes the dismutation of the superoxide anion (O2-) to H2O2 and O2. Superoxide-mediated damage has been implicated in a number of biological processes, including aging and cancer; however, it is not certain whether endogenously elevated levels of SOD will reduce the pathological events resulting from such damage. To understand the in vivo relationship between an efficient dismutation of O2- and oxidative injury to biological structures, we generated transgenic strains of Drosophila melanogaster overproducing CuZn SOD. This was achieved by microinjecting Drosophila embryos with P-elements containing bovine CuZn SOD cDNA under the control of the Drosophila actin 5c gene promoter. Adult flies of the resulting transformed lines which expressed both mammalian and Drosophila CuZn SOD were then used as a novel model for evaluating the role of oxygen radicals in aging. Our data show that expression of enzymatically active bovine SOD in Drosophila flies confers resistance to paraquat, an O2(-)-generating compound. This is consistent with data on adult mortality, because there was a slight but significant increase in the mean lifespan of several of the transgenic lines. The highest level of expression of the active enzyme in adults was 1.60 times the normal value. Higher levels may have led to the formation of toxic levels of H2O2 during development, since flies that died during the process of eclosion showed an unusual accumulation of lipofuscin (age pigment) in some of their cells. In conclusion, our data show that free-radical detoxification has a minor by positive effect on mean longevity for several strains.
Mol Cell Biol 1991 Feb
PMID:Expression of bovine superoxide dismutase in Drosophila melanogaster augments resistance of oxidative stress. 189 85


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>